If You Only Knew
by Flutemelody
Summary: Something is over taken the Doctor's mind. The Doctor is forgetting things that is haunting Amy, things that he done to her. How can he fix a broken trust he broke, when he doesn't know what he did to break it? DARK/RATED M AMY/11th Slightly OOC  maybe
1. Chapter 1

I'm worried about posting this story. This is my first Doctor Who story. I didn't want to write a story for Doctor who, cause I knew I can't live up to the ones on this site, but this story wouldn't leave my head so I wrote it down. . .

_I'll need a Beta for this story, cause as you'll see my grammar will lack horrorible. _PM if you're willing.

This is set after Stones and flesh, but no they didn't go get Rory. (Note; I'm not a big fan of Rory, but I will never bash him.)

Should I keep going or not?

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Amy sighed and pounded her head against the wall she was leaning on. "I'm way in over my head, aren't I?" Amy asked out loud to the TARDIS. The feeling of being silly talking to the time machine pasted after only a few time of talking to TARDIS. Even though the TARDIS couldn't talk back, she had ways of answering. The only sound the TARDIS made was a low humming sound. Amy sighed again and closed her eyes. "I was terrified you were going to agree with that."

Only an hour ago, Amy had the Doctor pushed up against the TARDIS trying to kiss him. It was stupid of her, she shouldn't had let her emotions ruled her like that, but she had been scared and she wasn't in check of her emotions like she should had been.

_"I'm 907, and look at me! I don't get older, I just change; you get older, I don't. And this can't ever work." _ His words echoed inside her mind. It wouldn't ever work between them, she knew that, but she had made a mistake. She had fallen in love with him.

She opened her eyes as a single tear fell. This was wrong, she already knew that. Back home, she had her life set for her. She was going to get married and live a happy life with Rory. _'But, can I live a happy life with Rory when my heart doesn't belong to him anymore?' _She thought and sighed when she didn't know the answer to that question.

"What am I to do now?" She asked the TARDIS. As if the TARDIS was answering her, the lights in the hallway she was standing in, blinked out and the TARDIS lit up a new hallway that wasn't there a few seconds ago. "I take it you want me to follow it?" She asked. The TARDIS give no signs of answering her, but a low humming sound.

"Well then, let's follow the scary hallway that could lead anywhere, why don't I." She murmured as she slowly made her way down the hall and she wondered where the TARDIS was guiding her to. After a few minutes, the lights flicked off all but one, lighting up a door that was a grayish blue. Amy cocked her head to the side, why had the TARDIS brought her here? She had no idea what was behind that door, but she had a feeling it was the Doctor.

Slowly she made her way toward the door, even though something inside her told her not to. As she reached for the doorknob and touched it, she jerked back as something shocked her. "Bloody hell," She hissed as she felt her hand burned. "Well that's rubbish; you lead me here, just so I can get my hand burned." She growled at the TARDIS as the door in front of her swing opened to show the Doctor standing there with his usual grin in place.

"Pond, what are you doing here? How did you even find my room?" He asked her shaking his head at her. Amy narrowed her eyes at the grinning Doctor, but answered him anyways. "The TARDIS lead me here." She said as she gritted her teeth. "Why did your door bloody shock me?" She asked him. The Doctor laughed.

"Cause, silly Pond, I can't have things wondering into my room while I'm sleep. Even I need my beauty sleep." He said with a laugh as he pulled at his hair. Amy just stared at him. "So tell me, there has to be a reason the TARDIS brought you here. Never had she lead a companion of mine to my bedroom before."

"Um," Amy said as she had tried to come up with a lie. "No Pond, don't lie to me. Do you not trust me, or something?" He asked her in a low voice, his grin slowly fading.

"You don't always tell me the truth." She snapped back at him. "Sometimes it's better not to tell the whole truth." He told her. "Now, let's get back to my question, please."

She just rolled her eyes, but didn't say anything. "Amelia," He said as he took a step toward her. "Doctor," She said back, not backing down. The grin on the Doctor face was long gone now and was replaced with a hard frown that reached his eyes. "You're not going to tell me, are you?" He asked taking another step toward her, and rested his forehead onto hers and looked into her eyes.

"You already know," She said after a long minute. The Doctor pulled back from her and cocked his head to the side. "I do?" He asked. Amy eyes flashed with fury, he was so thick headed sometimes.

"You do, and I'm not going to tell you. Figure it out yourself," She scowled at him and turned to walk away.

"It'll never work, Amelia. You don't understand. I'm not who you think I am. Please try and understand that."She kept walking away from him but said, "How do you know it'll never work unless you try?"

"Cause it just wouldn't. Please stop walking away and come back here so I can talk to you." He called after her. She stopped where she was, but didn't turn around. "Your human, I'm not. I have two hearts, and I don't age. Amy, you can spend the rest of your life with me, but I can't spend mine with you." She still didn't turn around to face him. But when she did turn around and faced the Doctor, fury clouded her eyes.

"You told me it wasn't going to work, don't you remember nor are you really that thick headed? I just want. . ." Amy Pond snapped at the Doctor, but trailed off at the end. The Doctor's face hardened like it was made of stone and something in him snapped and he let it take over him for a second. Just long enough, so it would scare Amy away from him. Amy saw it in his eyes as he was taken over by his dark side

In a blink of an eye, the Doctor was in front of her. His eyes were unreadable as he hissed words into her face. "I'm far from thick headed, Pond. I know what you want." With that, he claimed her lips with his own as she had done not an hour ago. Shocked and frightened, Amy tried to pull away from him, but he moved his arms around her body and restrained her with a determined grip that wouldn't loosen. "Come on, Amy. Isn't this what you wanted?" He grinned darkly at her, shadows of the hallways danced across his face showing her this wasn't the Doctor. Not her raggedy Doctor, but someone else inside him.

"No Doctor, this…this isn't you. Please." She begged as she had tried to him away again. "But this is where your wrong, Pond. This is me, I'm always this, I just learned to hide it. If you want me, you want this side too." He growled into her left ear. She tried again to push him away, and he let her do so.

"No," She sobbed as she caught her breath and walked away from him backways. "I don't believe this is you." She said with an uneven voice, but her eyes told him different and he smiled at that. He had scared her away from falling in love with him, something he had to do. Something he didn't want to do.

"Is that so?" He asked taking a step toward her and she took one back. He laughed. "Scared are we, Pond." He commented and turned around. "If I was you, I would run right about now. Back to your room, that is safe from me. I will not follow you, but if you stay around here in the empty hallways . . . Well let's just say, I can't promise you anything." With that he left.

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I really don't kow what made me write this, but I didn't know the Doctor was going to turn dark till after through this. Review.


	2. Chapter 2

If this is confusing, good I meant it to be. I promise to explain fully. . . Soon. :D

Still in need of a Beta. :/ PM me if you're willing.

_"Long for me as I for you, forgetting, what will be inevitable, the long black aftermath of pain."_

Malcolm Lowry

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The clock flashed 2:12, when Amy Pond had jerked awake and she quickly reached over and flicked her lamp on. Her eyes darted to the thing that had wakened her, a far off shadow in the corner of the room the TARDIS have let her stay in. Fear rang through her, but she didn't show it. At least her face didn't show the fear, but her eyes were a different story all together. "What are you doing here?" She asked, her voice only shook slightly.

Silence followed her question. A ghostly shadow moved from the dark in the room and the Doctor stood only five feet from her bed. "I asked you a question," Amy said again, her voice rang out clearly around the room as her fear died down a bit. The Doctor just shook his head and a smirk crawled across his face, wickedly.

"Do you plan on answering me?" Amy asked sitting up, the blanket that was wrapped around her fell slowly from her body. "Oi!" She snapped at him. And the Doctor's head snapped toward her as he was seeing her for the first time.

"Yes?" The Doctor asked shaking his head and looked around, the smirk on his face was gone now, replaced with a confused frown. "How…" He started to ask, but didn't and shook his head again to clear his thoughts. Amy stared at him, and raised an eyebrow at him.

"Never mind," He said quickly and turned to leave, but Amy stopped him by calling his name. He turned back and looked at her and waited for the questioning to start.

"Are you alright?" She asked, giving him her 'don't you dare give me rubbish' tone. He nodded and grinned Doctorie like at her. "Of course I am, silly Pond." He said to her, but his voice was lacking something. She just didn't know what. "You sure?" She asked again. "Yes, now excuse me…" He said as he quickly departed her room. Amy watched him go. She waited a few minutes before she got up and went looking for him.

The Doctor paced around the control room. He ran his hands through his hair madly as he thought. "I'm losing it, old girl." He told the TARDIS. "How did the bloody hell did I end up in Amy's room?" The TARDIS just hummed at him. "You're right," He said and did what she told him to do. Think back to last thing he could remember.

He remembered Amy kissing him. He had pulled her into the TARDIS and left her as he went to his room, but that was it. What happened to him to make him forget of how he ended up in Amy's bedroom. He kicked something on the floor as he heard a small voice behind him. "Doctor?" He didn't turn around. No, he was losing it and he couldn't let her know that. So he didn't turn around. "Go back to your room, Pond. We'll go somewhere tomorrow, like that planet you been asking to go to." He told her as he felt her eyes burn holes into his back.

"All right, Doctor." She turned to leave, but stopped. "I thought you said you weren't going to follow me back to my room? That I was going to be safe there." She said, and then fled out of view before he had time to ask what the hell she was talking about. He spun around too late to catch her.

"_Things just kept getting weirder_." The Doctor thought as he sighed. He was in need of a talk with Amelia Pond now.

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This is meant to be short. Bare with me, please. The plot line is changing for the better.


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